exprSetRG-class {arrayMagic} | R Documentation

## Class exprSetRG for two colour DNA microarray data (extension of exprSet)

### Description

This is a class representation for two colour DNA microarray data. The class is based on the class `exprSet` of the `Biobase` package. The red and green channels are stored in a single `exprSet` object. The information on the corresponding red-green pairs is stored separately. Several class methods offer a convienent way to access and set data.

### Creating Objects

`new('exprSetRG',`
`channels = ..., # object of class matrix with columns "green" and "red"`
`exprs = ..., # object of class matrix`
`se.exprs = ..., # object of class matrix`
`phenoData= ..., # object of class phenoData`
`notes = ..., # object of class character`
`annotation = ..., # object of class character`
`)`

### Slots

`indGreen`:
  Object of class `vector`; indexes of the green channel
`indRed`:
  Object of class `vector`; indexes of the red channel
`exprs`:
  Object of class `matrix`; the observed expression levels. This is a matrix with columns representing the red and green channels and rows representing genes. Each row in `channels` lists the indexes of the corresponding pair of red and green channels representing a single microarray slide.
`se.exprs`:
  Object of class `matrix`; this is a matrix of the same dimensions as `exprs`, e.g. useful to represent the standard error estimates for the corresponding expression levels.
`phenoData`:
  Object of class `phenoData`, i.e. an instance of class `phenoData` containing annotation information on the individual channels. The columns of the pData slot of this entity represent variables and the rows represent channels.
`notes`:
  Object of class `character` containing explanatory text; default: ""
`annotation`:
  Object of class `character`; default: ""

### Extends

Class `exprSet`, directly.

### Methods

show
  (exprSetRG): renders information about the exprSetRG in a concise way on stdout, cf. class exprSet.
getExprSetLogRatio
  (exprSetRG, seExprsHandling): Returns an `exprSet` object of the difference of the expression levels, i.e. the green channel minus the red channel. The `phenoData` slot it the result of calling the class method `phenoDataSlide` on the object `exprSetRG`. The `se.exprs` slot contains the root-mean-square or the mean of the se.exprs of both channels depending on the argument `seExprsHandling`. The root-mean-square might be useful if the two se.exprs values are estimated standard deviations based on the same number observations and identical distribution. `seExprsHandling` must be a character string; possible values are "rootMeanSquare" or "mean"; the default value is "rootMeanSquare".
getExprSetGreenMinusRed
  same as method `getExprSetLogRatio`
getExprSetRedMinusGreen
  similar to method `getExprSetLogRatio`; the "negative" difference of the expression levels is returned, i.e. the red channel minus the green channel.
getExprSetGreen
  (exprSetRG): Returns an `exprSet` object which contains the expression levels of the green channel and the corresponding annotation.
getExprSetRed
  (exprSetRG): Returns an `exprSet` object which contains the expression levels of the red channel and the corresponding annotation.
phenoDataSlide
  (exprSetRG): Returns an `phenoData` object characterizing all microarray slides. Those annotation information, which is the same for both channels (and not `NA`) is taken directly, e.g. the the slide number. All other annotation variables are added specifically for each channel, i.e. prefixed with "greenSpecific_" and "redSpecific_". Do not use varLabels-names for subsetting.
pDataSlide
  (exprSetRG): Returns an `pData` object, i.e. `pData(phenoDataSlide(exprSetRG))`; cf. `phenoDataSlide`. Do not use varLabels-names for subsetting.
phenoDataGreen
  (exprSetRG): Returns an `phenoData` object of the annotation information given for the green channel. Do not use varLabels-names for subsetting.
pDataGreen
  (exprSetRG): Returns the `pData` object taken out of the result of calling `phenoDataGreen`. Do not use varLabels-names for subsetting.
phenoDataRed
  (exprSetRG): Returns an `phenoData` object of the annotation information given for the red channel. Do not use varLabels-names for subsetting.
pDataRed
  (exprSetRG): Returns the `pData` object taken out of the result of calling `phenoDataRed`. Do not use varLabels-names for subsetting.
slideSubset
  (exprSetRG,i,j): Subsetting operation; where i corresponds to the rows and j corresponds to the microarray slides. j is given by indexes or logicals related to the order of the channel pairs in `channels`; cf. the constructor slot `channels`.
getIndGreen
  (exprSetRG): An accessor function for slot `indGreen`. The corresponding elements of indGreen and indRed define microarray slides.
getIndRed
  (exprSetRG): An accessor function for slot `indRed`. The corresponding elements of indGreen and indRed define microarray slides.
[
  (exprSetRG,i,j,type): A subset operator. Ensures that both the data and the annotation information (`phenoData`) are subseted properly. This may only mix up the pairing of the channels, i.e. the validity of an exprSetRG, if you use argument option type == "invalidExprSetRG". Default: "validExprSetRG".
cbind
  (...): Concatenates `exprSetRG` objects. Genes (rows) are assumed to match; cf. `cbind.exprSetRG`
as.exprSet
  (exprSetRG): Class cast, returns an object of `exprSet`, the information on the red and green channesl is discarded.

### Author(s)

Andreas Buness <a.buness@dkfz.de>

### See Also

`exprSet-class`, `arrayData-class`

### Examples

      indGreen=1:3
      indRed=4:6
      channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
      colnames(channels) <- c("green","red")
      eSA <- new("exprSetRG", exprs=matrix(1:60, ncol=6, nrow=10), phenoData=
              new("phenoData", pData=data.frame(matrix(0,nrow=6,ncol=1)),
                  varLabels=list(rep("varLabel1",1))), channels=channels)
      stopifnot( all(pDataSlide(eSA) ==pData(eSA)[1:3,,drop=FALSE]) )
      eSAGreen <- getExprSetGreen(eSA)
      eSARed <- getExprSetRed(eSA)
      eSALogRatio <- getExprSetLogRatio(eSA)
      eSALogRatio2 <- getExprSetGreenMinusRed(eSA)
      eSALogRatio3 <- getExprSetRedMinusGreen(eSA)
      stopifnot( identical( eSALogRatio, eSALogRatio2 ) )
      stopifnot( identical( exprs(eSALogRatio), exprs(eSAGreen)-exprs(eSARed)) )
      stopifnot( all.equal.numeric( exprs(eSALogRatio3), exprs(eSARed)-exprs(eSAGreen)) )
      eSAPart <- eSA[,c(1,3,1,4,6,4)]
      eSAInvalid <- eSA[,c(1,3,1,5,6,4),type="invalidExprSetRG"]
      eSAPart2 <- slideSubset(eSA,j=c(1,3,1))

      eSAeSA <- cbind(eSA, eSA)
      eSAeSAPart2 <- cbind(eSA, eSAPart2)
      stopifnot(is(as.exprSet(eSA), "exprSet"))

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